02171nas a2200193   4500008004100000022001400041245007900055210006900134260000800203300001200211490000700223520154000230100002201770700001801792700002001810700002001830700002001850856010701870       2024                        eng d  a1549-959600aImproved protein dynamics and hydration in the martini3 coarse-grain model0 aImproved protein dynamics and hydration in the martini3 coarsegr  cJAN  a837-8500 v643 a<p>
	The Martini coarse-grain force-field has emerged as an important framework to probe cellular processes at experimentally relevant time- and length-scales. However, the recently developed version, the Martini3 force-field with the implemented Go model (Martini3Go), as well as previous variants of the Martini model have not been benchmarked and rigorously tested for globular proteins. In this study, we consider three globular proteins, ubiquitin, lysozyme, and cofilin, and compare protein dynamics and hydration with observables from experiments and all-atom simulations. We show that the Martini3Go model is able to accurately model the structural and dynamic features of small globular proteins. Overall, the structural integrity of the proteins is maintained, as validated by contact maps, radii of gyration (Rg), and SAXS profiles. The chemical shifts predicted from the ensemble sampled in the simulations are consistent with the experimental data. Further, a good match is observed in the protein-water interaction energetics, and the hydration levels of the residues are similar to atomistic simulations. However, the protein-water interaction dynamics is not accurately represented and appears to depend on the protein structural complexity, residue specificity, and water dynamics. Our work is a step toward testing and assessing the Martini3Go model and provides insights into future efforts to refine Martini models with improved solvation effects and better correspondence to the underlying all-atom systems.</p>
1 aKharche, Shalmali1 aYadav, Manjul1 aHande, Vrushali1 aPrakash, Shikha1 aSengupta, Durba  uhttps://library.ncl.res.in/content/improved-protein-dynamics-and-hydration-martini3-coarse-grain-model